X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuhierarchycommand.cpp;h=07e3c1d0146ef521563697fe07deb38d7837b67d;hp=17e29d9528c1122f73a2f81a32c1998dded037cf;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6 diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp index 17e29d9..07e3c1d 100644 --- a/otuhierarchycommand.cpp +++ b/otuhierarchycommand.cpp @@ -12,11 +12,11 @@ //********************************************************************************************************************** vector OtuHierarchyCommand::setParameters(){ try { - CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput); - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -38,7 +38,7 @@ string OtuHierarchyCommand::getHelpString(){ helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n"; helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"; helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n"; - helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n"; return helpString; } catch(exception& e) { @@ -46,7 +46,21 @@ string OtuHierarchyCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string OtuHierarchyCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "otuheirarchy") { pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** OtuHierarchyCommand::OtuHierarchyCommand(){ try { @@ -67,6 +81,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -109,6 +124,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { abort = true; } }else if (listFile == "not open") { abort = true; } + else { m->setListFile(listFile); } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ @@ -159,56 +175,48 @@ int OtuHierarchyCommand::execute(){ } //map sequences to bin number in the "little" otu - map littleBins; + map littleBins; + vector binLabels0 = lists[0].getLabels(); for (int i = 0; i < lists[0].getNumBins(); i++) { if (m->control_pressed) { return 0; } - - string names = lists[0].get(i); - - //parse bin - while (names.find_first_of(',') != -1) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); - littleBins[name] = i; - } - - //get last name - littleBins[names] = i; - } + string bin = lists[0].get(i); + vector names; m->splitAtComma(bin, names); + for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; } + } ofstream out; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile)); + variables["[distance1]"] = lists[0].getLabel(); + variables["[tag]"] = "-"; + variables["[distance2]"] = lists[1].getLabel(); + string outputFileName = getOutputFileName("otuheirarchy",variables); m->openOutputFile(outputFileName, out); //go through each bin in "big" otu and output the bins in "little" otu which created it + vector binLabels1 = lists[1].getLabels(); for (int i = 0; i < lists[1].getNumBins(); i++) { - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; } - string names = lists[1].get(i); + string binnames = lists[1].get(i); + vector names; m->splitAtComma(binnames, names); //output column 1 - if (output == "name") { out << names << '\t'; } - else { out << i << '\t'; } + if (output == "name") { out << binnames << '\t'; } + else { out << binLabels1[i] << '\t'; } map bins; //bin numbers in little that are in this bin in big map::iterator it; //parse bin - while (names.find_first_of(',') != -1) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); - bins[littleBins[name]] = littleBins[name]; - } - - //get last name - bins[littleBins[names]] = littleBins[names]; + for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]]; } string col2 = ""; for (it = bins.begin(); it != bins.end(); it++) { if (output == "name") { col2 += lists[0].get(it->first) + "\t"; } - else { col2 += toString(it->first) + "\t"; } + else { col2 += binLabels0[it->first] + "\t"; } } //output column 2 @@ -217,10 +225,10 @@ int OtuHierarchyCommand::execute(){ out.close(); - if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; } m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); m->mothurOutEndLine();